I'm trying to use Mylyn to manage my assigned bugs in the Eclipse
bugzilla system. What is the expected workflow when you have changes
for multiple bugs in the same file?

For example, let's say I work on bug #1, and make some changes to
A.java, B.java and C.java. I make some progress, but get stuck, so I
move on to bug #2. That bug requires also requires changes to D.java
and also A.java.

What steps do I take so the changes for A.java in bug #2 can be
segregated from the changes for bug #1? The user guide leads me to
believe Mylyn can only handle changes at the file level, so I'm not
sure how I would go about keeping track of the changes without
collisions.

Is that what Attach Context is for?

I'm just getting started with Mylyn, so I may just be missing a common
use case here.